Nonuniversal scaling behavior of Barkhausen noise

We simulate Barkhausen avalanches on fractal clusters in a two-dimensional diluted Ising ferromagnet with an effective Gaussian random field. We vary the concentration of defect sites $c$ and find a scaling region for moderate disorder, where the distribution of avalanche sizes has the form $D(s,c,L) = s^{-(1+\tau (c))}{\cal{D}}(sL^{-D_s(c)})$. The exponents $\tau (c)$ for size and $\alpha (c)$ for length distribution, and the fractal dimension of avalanches $D_s(c)$ satisfy the scaling relation $D_s(c)\tau (c) =\alpha (c)$. For fixed disorder the exponents vary with driving rate in agreement with experiments on amorphous Si-Fe alloys.Comment: 5 pages, Latex, 4 PostScript figures include

Increases in sampling support the southern Gondwanan hypothesis for the origin of dinosaurs

Dinosaurs were ubiquitous in terrestrial ecosystems through most of the Mesozoic and are still diversely represented in the modern fauna in the form of birds. Recent efforts to better understand the origins of the group have resulted in the discovery of many new species of early dinosaurs and their closest relatives (dinosauromorphs). In addition, recent re-examinations of early dinosaur phylogeny have highlighted uncertainties regarding the interrelationships of the main dinosaur lineages (Sauropodomorpha, Theropoda and Ornithischia), and questioned the traditional hypothesis that the group originated in South Gondwana and gradually dispersed over Pangaea. Here, we use a historical approach to examine the impact of new fossil discoveries and changing phylogenetic hypotheses on biogeographic scenarios for dinosaur origins over 20 years of research time, and analyse the results in the light of different fossil record sampling regimes. Our results consistently optimize South Gondwana as the ancestral area for Dinosauria, as well as for more inclusive clades including Dinosauromorpha, and show that this hypothesis is robust to increased taxonomic and geographic sampling and divergent phylogenetic results. Our results do not find any support for the recently proposed Laurasian origin of dinosaurs and suggest that a southern Gondwanan origin is by far the most plausible given our current knowledge of the diversity of early dinosaurs and non-dinosaurian dinosauromorphs

Disorder-Induced Critical Phenomena in Hysteresis: Numerical Scaling in Three and Higher Dimensions

We present numerical simulations of avalanches and critical phenomena associated with hysteresis loops, modeled using the zero-temperature random-field Ising model. We study the transition between smooth hysteresis loops and loops with a sharp jump in the magnetization, as the disorder in our model is decreased. In a large region near the critical point, we find scaling and critical phenomena, which are well described by the results of an epsilon expansion about six dimensions. We present the results of simulations in 3, 4, and 5 dimensions, with systems with up to a billion spins (1000^3).Comment: Condensed and updated version of cond-mat/9609072,``Disorder-Induced Critical Phenomena in Hysteresis: A Numerical Scaling Analysis'

Hysteresis, Avalanches, and Disorder Induced Critical Scaling: A Renormalization Group Approach

We study the zero temperature random field Ising model as a model for noise and avalanches in hysteretic systems. Tuning the amount of disorder in the system, we find an ordinary critical point with avalanches on all length scales. Using a mapping to the pure Ising model, we Borel sum the $6-\epsilon$ expansion to $O(\epsilon^5)$ for the correlation length exponent. We sketch a new method for directly calculating avalanche exponents, which we perform to $O(\epsilon)$. Numerical exponents in 3, 4, and 5 dimensions are in good agreement with the analytical predictions.Comment: 134 pages in REVTEX, plus 21 figures. The first two figures can be obtained from the references quoted in their respective figure captions, the remaining 19 figures are supplied separately in uuencoded forma

Fair go? Indigenous rugby league players and the racial exclusion of the Australian national anthem

This article explores the implications of widely publicized national anthem protests by several Indigenous rugby league players in Australia during 2019. With a goal of doing justice to these Indigenous voices (and in this case also their silence), a critical race theory framework was deployed to both listen to, as well as interpret, the reasons behind the protests. The data source was online media reports that centered on the perspectives of players and rugby league officials, along with responses to the protests by prominent journalists and politicians via online opinion pieces. The findings indicate that the voices of Indigenous athletes in Australia are important in raising concerns about nationalist rituals and symbols that, by their colonialist nature, subjugate Aboriginal peoples. Importantly, the Indigenous rugby league players were not alone in their campaign. The Recognition in Anthem project, which began in 2017, indicates that the perspectives of these protesting rugby players were part of a wider discussion about change. The movement for a new national anthem, therefore, was not just isolated to sport, and this appears to have provided the Indigenous rugby players – as social commentators – with atypical influence

Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines

BACKGROUND: To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare cells found in the blood of patients with solid tumors and may play a key role in cancer dissemination. Uncovering CTC phenotypes offers a potential avenue to inform treatment. However, CTC transcriptional profiling is limited by leukocyte contamination; an approach to surmount this problem is single cell analysis. Here we demonstrate feasibility of performing high dimensional single CTC profiling, providing early insight into CTC heterogeneity and allowing comparisons to breast cancer cell lines widely used for drug discovery. METHODOLOGY/PRINCIPAL FINDINGS: We purified CTCs using the MagSweeper, an immunomagnetic enrichment device that isolates live tumor cells from unfractionated blood. CTCs that met stringent criteria for further analysis were obtained from 70% (14/20) of primary and 70% (21/30) of metastatic breast cancer patients; none were captured from patients with non-epithelial cancer (n = 20) or healthy subjects (n = 25). Microfluidic-based single cell transcriptional profiling of 87 cancer-associated and reference genes showed heterogeneity among individual CTCs, separating them into two major subgroups, based on 31 highly expressed genes. In contrast, single cells from seven breast cancer cell lines were tightly clustered together by sample ID and ER status. CTC profiles were distinct from those of cancer cell lines, questioning the suitability of such lines for drug discovery efforts for late stage cancer therapy. CONCLUSIONS/SIGNIFICANCE: For the first time, we directly measured high dimensional gene expression in individual CTCs without the common practice of pooling such cells. Elevated transcript levels of genes associated with metastasis NPTN, S100A4, S100A9, and with epithelial mesenchymal transition: VIM, TGFß1, ZEB2, FOXC1, CXCR4, were striking compared to cell lines. Our findings demonstrate that profiling CTCs on a cell-by-cell basis is possible and may facilitate the application of 'liquid biopsies' to better model drug discovery

Single-feature polymorphism discovery by computing probe affinity shape powers

<p>Abstract</p> <p>Background</p> <p>Single-feature polymorphism (SFP) discovery is a rapid and cost-effective approach to identify DNA polymorphisms. However, high false positive rates and/or low sensitivity are prevalent in previously described SFP detection methods. This work presents a new computing method for SFP discovery.</p> <p>Results</p> <p>The probe affinity differences and affinity shape powers formed by the neighboring probes in each probe set were computed into SFP weight scores. This method was validated by known sequence information and was comprehensively compared with previously-reported methods using the same datasets. A web application using this algorithm has been implemented for SFP detection. Using this method, we identified 364 SFPs in a barley near-isogenic line pair carrying either the wild type or the mutant <it>uniculm2 </it>(<it>cul2</it>) allele. Most of the SFP polymorphisms were identified on chromosome 6H in the vicinity of the <it>Cul2 </it>locus.</p> <p>Conclusion</p> <p>This SFP discovery method exhibits better performance in specificity and sensitivity over previously-reported methods. It can be used for other organisms for which GeneChip technology is available. The web-based tool will facilitate SFP discovery. The 364 SFPs discovered in a barley near-isogenic line pair provide a set of genetic markers for fine mapping and future map-based cloning of the <it>Cul2 </it>locus.</p

Ancestral Components of Admixed Genomes in a Mexican Cohort

For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study “virtual genomes” of admixed individuals. We apply this approach to a cohort of 492 parent–offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations—Africa, Europe, and America—vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10–15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people

Identification of genes differentially expressed in a resistant reaction to Mycosphaerella pinodes in pea using microarray technology

<p>Abstract</p> <p>Background</p> <p>Ascochyta blight, caused by <it>Mycosphaerella pinodes </it>is one of the most important pea pathogens. However, little is known about the genes and mechanisms of resistance acting against <it>M. pinodes </it>in pea. Resistance identified so far to this pathogen is incomplete, polygenic and scarce in pea, being most common in <it>Pisum </it>relatives. The identification of the genes underlying resistance would increase our knowledge about <it>M. pinodes-</it>pea interaction and would facilitate the introgression of resistance into pea varieties. In the present study differentially expressed genes in the resistant <it>P. sativum </it>ssp. <it>syriacum </it>accession P665 comparing to the susceptible pea cv. Messire after inoculation with <it>M. pinodes </it>have been identified using a <it>M. truncatula </it>microarray.</p> <p>Results</p> <p>Of the 16,470 sequences analysed, 346 were differentially regulated. Differentially regulated genes belonged to almost all functional categories and included genes involved in defense such as genes involved in cell wall reinforcement, phenylpropanoid and phytoalexins metabolism, pathogenesis- related (PR) proteins and detoxification processes. Genes associated with jasmonic acid (JA) and ethylene signal transduction pathways were induced suggesting that the response to <it>M. pinodes </it>in pea is regulated via JA and ET pathways. Expression levels of ten differentially regulated genes were validated in inoculated and control plants using qRT-PCR showing that the P665 accession shows constitutively an increased expression of the defense related genes as peroxidases, disease resistance response protein 39 (DRR230-b), glutathione S-transferase (GST) and 6a-hydroxymaackiain methyltransferase.</p> <p>Conclusions</p> <p>Through this study a global view of genes expressed during resistance to <it>M. pinodes </it>has been obtained, giving relevant information about the mechanisms and pathways conferring resistance to this important disease. In addition, the <it>M. truncatula </it>microarray represents an efficient tool to identify candidate genes controlling resistance to <it>M. pinodes </it>in pea.</p

Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper